Genome-Wide Identification of the GRAS Transcription Factor Family in Coptis chinensis Reveals Tissue-Specific Co-Expression with bZIP Proteins Under Light Stress

GRAS transcription factors are essential for plant growth and stress adaptation, yet they remain uncharacterized in the medicinal herb Coptis chinensis. To address this gap, we performed a genome-wide identification of the GRAS family and investigated its transcriptional responses to temperature and light stress, integrating comparative transcriptomics with promoter analysis to explore potential co-expression with bZIP factors. A total of 48 CcGRAS genes were identified and found to be unevenly distributed across nine chromosomes. Expression profiling revealed that CcGRAS genes are markedly more responsive to varying light intensities (476, 8340 lx) than to temperature stresses (15, 35 °C), relative to controls (2060 lx for light, 25 °C for temperature). Co-expression analysis uncovered an underground tissue-specific module in which CcbZIP16 is upregulated with four CcGRAS genes (CcGRAS11, CcGRAS12, CcGRAS43, CcGRAS48) that are coordinately upregulated specifically under low-light conditions. The promoters of these co-expressed genes are significantly enriched in canonical light-responsive cis-elements, providing correlative evidence for their coordinated transcriptional control. Together, these findings identify a tissue-specific GRAS-bZIP co-expressed gene set under light stress and suggest a candidate regulatory framework for dissecting light adaptation mechanisms. This work also provides a foundation for targeted genetic improvements in stress tolerance and alkaloid biosynthesis in this important medicinal plant.